Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure

Piscirickettsia salmonisis the causative bacterial pathogen of piscirickettsiosis, a salmonid disease that causes notable mortalities in the worldwide aquaculture industry. Published research describes the phenotypic traits, virulence factors, pathogenicity and antibiotic‐resistance potential for various P. salmonisstrains. However, evolutionary and genetic information is scarce for P. salmonis. The present study used multilocus sequence typing (MLST) to gain insight into the population structure and evolution of P. salmonis. Forty‐two Chilean P. salmonisisolates, as well as the type strain LF‐89^T, were recovered from diseased Salmo salar, Oncorhynchus kisutchand Oncorhynchus mykissfrom two Chilean Regions. MLST assessed the loci sequences of dnaK, efp, fumC, glyA, murG, rpoD and trpB. Bioinformatics analyses established the genetic diversity among P. salmonis isolates (H = 0.5810). A total of 23 sequence types (ST) were identified, 53.48% of which were represented by ST1, ST5 and ST2. Population structure analysis through polymorphism patterns showed few polymorphic sites (218 nucleotides from 4,010 bp), while dN/dS ratio analysis indicated purifying selection for dnaK, epf, fumC, murG, and rpoD but neutral selection for the trpB loci. The standardized index of association indicated strong linkage disequilibrium, suggesting clonal population structure. However, recombination events were detected in a group of seven isolates. Findings included genogroups homologous to the LF‐89^T and EM‐90 strains, as well as a seven‐isolate hybrid genogroup recovered from both assessed regions (three O. mykiss and four S. salar isolates). The presented MLST scheme has comparative potential, with promising applications in studying distinct P. salmonis isolates (e.g., from different hosts, farms, geographical areas) and in understanding the epidemiology of this pathogen.     

Associations between morphometric variables and weight and yields carcass in Pirapitinga Piaractus brachypomus

The objective of this work was to evaluate the association between morphometric variables and carcass characteristics in Pirapitinga. We used a thousand specimens of Pirapitinga with an average weight of 1,200 g, which were stunned, slaughtered, weighed, measured, and processed for morphometric and processing yield analysis, to obtain weights, carcass and fillet yields. Initially, the linearity of the variables was verified. Pearson's simple and partial correlation tests were performed between all metrics. Track analysis was performed considering the weights and yields of carcass and filet as dependent variables and the others as independent variables. Ridge regression models were used to eliminate the effects of multicollinearity among the independent variables. Observations showed that the simple correlations between body weights and yields were superior to the partial ones in terms of magnitude. The length and circumference of the specimens were the measures most linearly associated with weight, carcass weight and fillet with rib weight. As for carcass yield and fillet yield, linear correlation coefficients were low and not significant when associated with body weights. With the path analysis, we could observe significant positive correlations between the morphometric measurements for weight, carcass weight and fillet with rib weight. The standard length, body circumference and body circumference/body height ratio are the most correlated. The latter are the most important variables in the evaluation of body weights in Pirapitinga fish. They can serve as criteria for indirect selection in searching for fish with better carcass characteristics. As for fillet and carcass yields, the morphometric variables have not shown to be efficient for indirect selection.     

Developments in the nutrition of Menidia estor Jordan 1880

The Mexican silverside, Menidia estor, is a species with great regional importance and with very high prices in local markets. Unfortunately, due to high fisheries pressure, environmental degradation and pollution, the species has become endangered. Recently, there has been much progress in the biotechnology of this species, aimed at its culture, and the present paper describes the advances in feeding and nutrition of those important fish. M. estor is a stomachless, zooplantophagous fish, which also occasionally feeds on small fish and crustaceans in the adult stage. Studies on the digestive enzymatic activities show high proteolytic capacity and a late or different model of digestive maturation from that described for marine stomach fish. Nutritional studies on M. estor have shown that juveniles have dietary requirements of about 400 g kg^?1 protein and 80 mg kg^?1 vitamin C. The upper level of dietary carbohydrate for good growth and survival for juveniles is about 150 g kg^?1. Based on the high docosahexaenoic acid (DHA) content in flesh when fed on diets low in DHA, it is believed that the species has the capacity to biosynthetize >20‐carbon fatty acids from 18‐carbon fatty acids. The high levels of DHA in flesh makes this fish a very significant potential component of human nutrition. Using these findings the first practical diets for commercial culture of the species have been developed.     

Genetic divergence among gerbera accessions evaluated by RAPD

Genetic diversity was evaluated by RAPD markers and morpho-agronomic characters for a total of 42 accessions of Barberton daisy (Gerbera jamesonii) consisting of 29 commercial and 13 wild accessions. A total of 74 polymorphic bands were obtained employing a set of 12 primer pairs. The average genetic similarity coefficient for the 42 accessions, evaluated by Jaccard index was 0.55 ranging from 0.28 to 1.00. The genetic structure found among Barberton daisy accessions was evaluated by hierarchic classification analyses and UPGMA modeling, revealing six clusters of genotypes where two of them include the wild accessions and the remaining four including commercial material, except for wild genotype number 9. Shannon (H′) index was calculated using the molecular markers to investigate the genetic variation among the Gerbera accessions and showed higher values for the commercial cluster in comparison to the values obtained for the individuals from the non-commercial cluster, namely 0.34 versus 0.27, respectively. Therefore, both calculated indices (Jaccard and Shannon) indicated the presence of higher genetic variation among commercial accessions in comparison to the cluster representing non-commercial accessions, suggesting that genetic breeding programs may focus on commercial accessions to recombine interesting genotypes with commercially important and marketing-desired characteristics.     

Slow fiber cluster pattern in pig longissimus thoracis muscle: implications for myogenesis

Recent evidence implicates fiber type proportions as playing a role in meat eating quality, and in pigs it has been suggested that the slow oxidative fibers contribute to both juiciness and tenderness. The fiber distribution in pigs is different from that found in most other species, in which the various types of skeletal muscle fiber are distributed in a "checkerboard" pattern, because in pigs the slow oxidative fibers have a clustered distribution. The initial processes leading to fiber clustering are likely to occur during myogenesis, but the precise mechanistic aetiology of this patterning and whether the slow oxidative fiber clusters occur in a random or ordered fashion is unknown. In the present study longissimus thoracis muscle from Large White crossbred pigs was sampled at the 10th rib, 48 h postmortem. Transverse cryo-sections were cut and histochemically stained to allow the identification of the main muscle fiber types: slow oxidative, fast glycolytic, and fast oxidative glycolytic. Images of the sections were captured and analyzed using point processes and Voronoi Tesselations to examine the randomness and spatial distribution of the clusters of slow oxidative fibers found in pig longissimus thoracis muscle. The results showed that an assumption of complete spatial randomness can be rejected and that a mathematical model incorporating a minimum distance of 1.7 to 2.0 microm between cluster centers produced fiber patterns similar to those observed in the original transverse sections of the muscle. In addition, if it assumed that the central fiber in each cluster is derived from primary myoblast progenitors, these results suggest that there may be some degree of repulsion between the primary fibers during the initial stages of cluster formation. The mechanistic basis of such repulsion is not clear, but it is speculated that secreted factors, such as sonic hedgehog or myostatin may play a role.     

Leptin and leptin receptors during malaria infection in mice

Leptin, which is involved in a range of physiological processes, could be an important factor in the pathogenesis of malaria. We found that levels of leptin in serum and urine in Plasmodium berghei-infected mice increased progressively after infection, reaching a maximum value on day 6 post-infection. Serum values were approximately five-fold higher in infected mice than in non-infected controls. A similar relation was found for values of leptin in urine. Soluble leptin receptor levels also increased significantly in serum, more or less in line with the leptin increase. Our work represents the first report of visibly augmented leptin and soluble leptin receptor secretion in malarial infection.     

Promoting and preserving biodiversity in the urban forest

Efforts at mitigating global biodiversity loss have often focused on preserving large, intact natural habitats. However, preserving biodiversity should also be an important goal in the urban environment, especially in highly urbanized areas where little natural habitat remains. Increasingly, research at the city/county scale as well as at the landscape scale reveals that urban areas can contain relatively high levels of biodiversity. Important percentages of species found in the surrounding natural habitat, including endangered species, have been found in the urban forest.

This contribution concisely highlights some examples of urban biodiversity research from various areas of the world. Key issues involved in understanding the patterns and processes that affect urban biodiversity, such as the urban–rural gradient and biotic homogenization, are addressed. The potential for urban areas to harbor considerable amounts of biodiversity needs to be recognized by city planners and urban foresters so that management practices that preserve and promote that diversity can be pursued. Management options should focus on increasing biodiversity in all aspects of the urban forest, from street trees to urban parks and woodlots.     

Electro-acupuncture and Chinese herbs for treatment of cervical intervertebral disk disease in a dog

A non-ambulatory dog with tetraparesis following a pain episode that had evolved over 2 months was submitted for medical treatment and diagnosed with intervertebral disk disease at C3-C4 and dorsal extradural compression at C1-C2 and C3-C4 using myelography and computed tomography. The dog experienced ambulation recovery after 15 days of treatment with only electroacupuncture and Chinese herbal medicine, with marked improvement occurring after only 10 treatments. Six months of follow-up demonstrated that the dog was stable and had no recurrence of symptoms. Therefore, it was concluded that the combination of electroacupuncture and Chinese herbal medicine was responsible for motor rehabilitation.     

Evaluation of electroacupuncture treatment for thoracolumbar intervertebral disk disease in dogs

OBJECTIVE: To evaluate use of electroacupuncture combined with standard Western medical treatment versus Western medical treatment alone for treatment of thoracolumbar intervertebral disk disease in dogs. DESIGN: Prospective controlled study. ANIMALS: 50 dogs with signs of thoracolumbar intervertebral disk disease. PROCEDURES: Dogs were randomly allocated to 1 of 2 treatment groups and classified as having grade 1 to 5 neurologic dysfunction. Dogs in group 1 received electroacupuncture stimulation combined with standard Western medical treatment; those in group 2 received only standard Western medical treatment. A numeric score for neurologic function was evaluated at 4 time points to evaluate effects of treatments. RESULTS: Time (mean +/- SD) to recover ambulation in dogs with grade 3 and 4 dysfunction in group 1 (10.10 +/- 6.49 days) was significantly lower than in group 2 (20.83 +/- 11.99 days). Success (able to walk without assistance) rate for dogs with grade 3 and 4 dysfunction in group 1 (10/10 dogs) was significantly higher than that of similarly affected dogs in group 2 (6/9 dogs). Dogs without deep pain perception (grade 5 dysfunction) had a success (recovery of pain sensation) rate of 3 of 6 and 1 of 8 in groups 1 and 2, respectively, but the difference was not significant. Overall success rate (all dysfunction grades) for group 1 (23/26; 88.5%) was significantly higher than for group 2 (14/24; 58.3%). CONCLUSIONS AND CLINICAL RELEVANCE: Electroacupuncture combined with standard Western medical treatment was effective and resulted in shorter time to recover ambulation and deep pain perception than did use of Western treatment alone in dogs with signs of thoracolumbar intervertebral disk disease.